title: Great ape genetic diversity and population history.
abstract: Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
authors.affiliation: Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Prado-Martinez
authors.forename: Peter H
authors.initials: PH
authors.lastname: Sudmant
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Kidd
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Kelley
authors.forename: Belen
authors.initials: B
authors.lastname: Lorente-Galdos
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Veeramah
authors.forename: August E
authors.initials: AE
authors.lastname: Woerner
authors.forename: Timothy D
authors.initials: TD
authors.lastname: O'Connor
authors.forename: Gabriel
authors.initials: G
authors.lastname: Santpere
authors.forename: Alexander
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authors.lastname: Cagan
authors.forename: Christoph
authors.initials: C
authors.lastname: Theunert
authors.forename: Ferran
authors.initials: F
authors.lastname: Casals
authors.forename: Hafid
authors.initials: H
authors.lastname: Laayouni
authors.forename: Kasper
authors.initials: K
authors.lastname: Munch
authors.forename: Asger
authors.initials: A
authors.lastname: Hobolth
authors.forename: Anders E
authors.initials: AE
authors.lastname: Halager
authors.forename: Maika
authors.initials: M
authors.lastname: Malig
authors.forename: Jessica
authors.initials: J
authors.lastname: Hernandez-Rodriguez
authors.forename: Irene
authors.initials: I
authors.lastname: Hernando-Herraez
authors.forename: Kay
authors.initials: K
authors.lastname: Prüfer
authors.forename: Marc
authors.initials: M
authors.lastname: Pybus
authors.forename: Laurel
authors.initials: L
authors.lastname: Johnstone
authors.forename: Michael
authors.initials: M
authors.lastname: Lachmann
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.forename: Dorina
authors.initials: D
authors.lastname: Twigg
authors.forename: Natalia
authors.initials: N
authors.lastname: Petit
authors.forename: Carl
authors.initials: C
authors.lastname: Baker
authors.forename: Fereydoun
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Marcos
authors.initials: M
authors.lastname: Fernandez-Callejo
authors.forename: Marc
authors.initials: M
authors.lastname: Dabad
authors.forename: Michael L
authors.initials: ML
authors.lastname: Wilson
authors.forename: Laurie
authors.initials: L
authors.lastname: Stevison
authors.forename: Cristina
authors.initials: C
authors.lastname: Camprubí
authors.forename: Tiago
authors.initials: T
authors.lastname: Carvalho
authors.forename: Aurora
authors.initials: A
authors.lastname: Ruiz-Herrera
authors.forename: Laura
authors.initials: L
authors.lastname: Vives
authors.forename: Marta
authors.initials: M
authors.lastname: Mele
authors.forename: Teresa
authors.initials: T
authors.lastname: Abello
authors.forename: Ivanela
authors.initials: I
authors.lastname: Kondova
authors.forename: Ronald E
authors.initials: RE
authors.lastname: Bontrop
authors.forename: Anne
authors.initials: A
authors.lastname: Pusey
authors.forename: Felix
authors.initials: F
authors.lastname: Lankester
authors.forename: John A
authors.initials: JA
authors.lastname: Kiyang
authors.forename: Richard A
authors.initials: RA
authors.lastname: Bergl
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Lonsdorf
authors.forename: Simon
authors.initials: S
authors.lastname: Myers
authors.forename: Mario
authors.initials: M
authors.lastname: Ventura
authors.forename: Pascal
authors.initials: P
authors.lastname: Gagneux
authors.forename: David
authors.initials: D
authors.lastname: Comas
authors.forename: Hans
authors.initials: H
authors.lastname: Siegismund
authors.forename: Julie
authors.initials: J
authors.lastname: Blanc
authors.forename: Lidia
authors.initials: L
authors.lastname: Agueda-Calpena
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.forename: Lucinda
authors.initials: L
authors.lastname: Fulton
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Tishkoff
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Ivo G
authors.initials: IG
authors.lastname: Gut
authors.forename: Mary Katherine
authors.initials: MK
authors.lastname: Gonder
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.forename: Arcadi
authors.initials: A
authors.lastname: Navarro
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Akey
authors.forename: Jaume
authors.initials: J
authors.lastname: Bertranpetit
authors.forename: David
authors.initials: D
authors.lastname: Reich
authors.forename: Thomas
authors.initials: T
authors.lastname: Mailund
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.forename: Christina
authors.initials: C
authors.lastname: Hvilsom
authors.forename: Aida M
authors.initials: AM
authors.lastname: Andrés
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Wall
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hammer
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
mesh_terms: D000349:Africa; D000818:Animals; D000835:Animals, Wild / Q000235:genetics; D000836:Animals, Zoo / Q000235:genetics; D001210:Asia, Southeastern; D019143:Evolution, Molecular; D051456:Gene Flow / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome / Q000235:genetics; D006071:Gorilla gorilla / Q000145:classification / Q000235:genetics; D015186:Hominidae / Q000145:classification / Q000235:genetics*; D006801:Humans; D007178:Inbreeding; D019974:Pan paniscus / Q000145:classification / Q000235:genetics; D002679:Pan troglodytes / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011156:Population Density